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I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

updated jmol-app.zip and SwingJS-site.zip

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JAL-3626 issue #2 - Jmol not loading from JVP

- just a versioning issue with core_jvjmol

- updated jmol-app.zip

- updated SwingJS-site.zip

- buildcore.xml creates core_jvjmol.z.js

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MiGLayout and VARNA site zips for SwingJS 3.2.9

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removing impossible test for intvervalstore containing a string

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JAL-3253 SwingJS-32.9.v1e

- Platform upgrade

- SwingJS upgrade

- java2script upgrade

- test fixes for thread concurrency

SwingJS runtime update 3.2.9-v1b

- mostly fixes from recent SwingJS work involving

-- expanded FileSystem and temp file management

-- super-fast HashMap (faster than Java!), HashTable,

StringBuilder, StringBuffer, NumberFormat, DecimalFormat

-- improved ResourceBundle

-- full Locale information

-- additional BufferedImage/ColorModel/Raster support

- fixes temp files not cached (JSTempFile, for Jmol)

- fixes AbstractStringBuilder.replace() typo

- reverts recent HashSet acceleration due to Jalview

using String.hashCode() for display order of features

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jmol.app.zip and SwingJS-site.zip; java2script 3.2.9-v1b

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JAL-3559 temporary branch adding JS files complete

    • binary
    ./MiGLayout-site.zip
    • binary
    ./intervalstore-site.zip
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updated interval-site.zip

Java 11 integration;

-- compiler complaining about javax.xml module

Failed to resolve resource /.build_properties:

@swingjs/j2s/jalview/bin/Cache.js:164:24

transpiler was 3.2.9-v1 now 3.2.4.07 for net.miginfocom.swing.MigLayout

TypeError: C$.UNIT_MAP.put$TK$TV is not a function

-- some runtime errors involving resources

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jmol-app.zip update for java2script 3.2.5.v1

Revert "JAL-3210 Moving j2s components around"

This reverts commit ea88f37133ba49aca6cd7bf0cc4242c0594cebf1.

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JAL-3210 Moving j2s components around

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JAL-3210 Moving j2s components around

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JAL-3397 updated intervalstore-site from intervalstore-1.1 source

I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit ...

I have added a large number of commits to this review which were tagged "JAL-3253-applet" or "Jalview-JS/develop-3253" or similar. This should be just the issue id for JIRA to associate the commit with the issue.

This reset also needs to happen in copyAlignPanel() (which also calls loadViewport() where the flag is set on).

This reset also needs to happen in copyAlignPanel() (which also calls loadViewport() where the flag is set on).

JAL-3210 Barebones gradle/buildship/eclipse. See README

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new SwingJS-site.zip fixes menu persistence issues

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Can't reproduce this now (can't "bring desktop to front"). Will resolve and reopen if it recurs.

Can't reproduce this now (can't "bring desktop to front"). Will resolve and reopen if it recurs.

Jalview-JS/JAL-3253-applet fix for original desktop, centralizing regex and loadStaticResource

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Jalview-JS/JAL-3253-applet also comments relating to JAL-3268

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No proprietary format files please! Is this meant to be a temporary working record or a permanent one. If the latter, can it be in csv or tsv format?

No proprietary format files please! Is this meant to be a temporary working record or a permanent one. If the latter, can it be in csv or tsv format?

No problem, the call to ScoreModels.getInstance() is unchanged, only how it is implemented.

No problem, the call to ScoreModels.getInstance() is unchanged, only how it is implemented.

Deferred to JAL-3265

Deferred to JAL-3265

Failing test getValidSourceDBRefExceptionXTest() (Network not Functional test). Now throws NullPointerException but coded only to expect SiftsException. Traced to uninitialized field DBRefEntry.ucv...

Failing test getValidSourceDBRefExceptionXTest() (Network not Functional test).
Now throws NullPointerException but coded only to expect SiftsException.
Traced to uninitialized field DBRefEntry.ucversion. Initialising this to "" (like version) resolves this.

I am nervous of doing much processing in a static block in case of errors giving ExceptionInInitializerError. Also possible dependency on order of classloading if one class's static codes reference...

I am nervous of doing much processing in a static block in case of errors giving ExceptionInInitializerError.
Also possible dependency on order of classloading if one class's static codes references another's.
Maybe move back to inside constructor?
In fact, was there any need to change this class from the 'standard' singleton pattern, if we don't want it "per applet"?

? there are no tests that call this getInstance() for this class. And if there were they would normally be in the same package so the method could be either package private, or called by reflection.

? there are no tests that call this getInstance() for this class. And if there were they would normally be in the same package so the method could be either package private, or called by reflection.

I am seeing some odd z-plane behaviour, not sure if it is specific to this branch. If the desktop is brought to front, I can't then bring any other panel to front.

I am seeing some odd z-plane behaviour, not sure if it is specific to this branch. If the desktop is brought to front, I can't then bring any other panel to front.